1clz: Difference between revisions

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[[Image:1clz.gif|left|200px]]<br /><applet load="1clz" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1clz, resolution 2.8&Aring;" />
'''IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER'''<br />


==Overview==
==IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER==
<StructureSection load='1clz' size='340' side='right'caption='[[1clz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1clz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CLZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CLZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NON:METHYL+NONANOATE+(ESTER)'>NON</scene>, <scene name='pdbligand=PRD_900054:Lewis+Y+antigen,+beta+anomer'>PRD_900054</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1clz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1clz OCA], [https://pdbe.org/1clz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1clz RCSB], [https://www.ebi.ac.uk/pdbsum/1clz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1clz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IGHG3_MOUSE IGHG3_MOUSE]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cl/1clz_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1clz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of the murine BR96 Fab and its human chimera have been determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey) at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a large pocket which is formed by residues of all CDR loops except L2. The binding of the carbohydrate is mediated predominantly by aromatic residues in BR96. Analysis of the structure suggests that BR96 is capable of recognizing a structure larger than the Le(y) tetrasaccharide, providing a possible explanation for its high tumour selectivity. The structure provides a rationale for mutagenesis experiments that have resulted in BR96 CDR loop mutants with increased affinity for nLey and/or tumour cells.
The crystal structures of the murine BR96 Fab and its human chimera have been determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey) at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a large pocket which is formed by residues of all CDR loops except L2. The binding of the carbohydrate is mediated predominantly by aromatic residues in BR96. Analysis of the structure suggests that BR96 is capable of recognizing a structure larger than the Le(y) tetrasaccharide, providing a possible explanation for its high tumour selectivity. The structure provides a rationale for mutagenesis experiments that have resulted in BR96 CDR loop mutants with increased affinity for nLey and/or tumour cells.


==About this Structure==
The x-ray structure of an anti-tumour antibody in complex with antigen.,Jeffrey PD, Bajorath J, Chang CY, Yelton D, Hellstrom I, Hellstrom KE, Sheriff S Nat Struct Biol. 1995 Jun;2(6):466-71. PMID:7664109<ref>PMID:7664109</ref>
1CLZ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=NON:'>NON</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CLZ OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The x-ray structure of an anti-tumour antibody in complex with antigen., Jeffrey PD, Bajorath J, Chang CY, Yelton D, Hellstrom I, Hellstrom KE, Sheriff S, Nat Struct Biol. 1995 Jun;2(6):466-71. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7664109 7664109]
</div>
<div class="pdbe-citations 1clz" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Protein complex]]
[[Category: Bajorath J]]
[[Category: Bajorath, J.]]
[[Category: Sheriff S]]
[[Category: Sheriff, S.]]
[[Category: NON]]
[[Category: glycoprotein]]
[[Category: immunoglobulin c region]]
[[Category: transmembrane]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:07:29 2008''
Retrieved from "https://proteopedia.org/1clz"